Fast identification of Escherichia coli in urinary tract infections using a virulence gene based PCR approach in a novel thermal cycler

Brons, Jolanda K.; Vink, Stefanie N.; Vos, Marjon G. J. de; Reuter, Stefan; Dobrindt, Ulrich; Elsas, Jan Dirk van

doi:10.1016/j.mimet.2019.105799

Cited by 30 publications

(23 citation statements)

References 47 publications

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“…Supernatants were discarded and pellets dissolved in 100 μl sterile dH2O which was then used for DNA extraction. DNA extractions were performed using the fast DNA extraction method described by Brons et al (2020) , based on the Qiagen PCR purification kit (Qiagen, Hilden, Germany). Three Escherichia coli , two Corynebacterium, and the two Lactobacillus jensenii isolates had a too low yield as evidenced from gel electrophoresis (PCR performed using primers B8F and 1492R).…”

Section: Methodsmentioning

confidence: 99%

The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens

et al. 2021

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The human body harbors numerous populations of microorganisms in various ecological niches. Some of these microbial niches, such as the human gut and the respiratory system, are well studied. One system that has been understudied is the urinary tract, primarily because it has been considered sterile in the absence of infection. Thanks to modern sequencing and enhanced culture techniques, it is now known that a urinary microbiota exists. The implication is that these species live as communities in the urinary tract, forming microbial ecosystems. However, the interactions between species in such an ecosystem remains unknown. Various studies in different parts of the human body have highlighted the ability of the pre-existing microbiota to alter the course of infection by impacting the pathogenicity of bacteria either directly or indirectly. For the urinary tract, the effect of the resident microbiota on uropathogens and the phenotypic microbial interactions is largely unknown. No studies have yet measured the response of uropathogens to the resident urinary bacteria. In this study, we investigate the interactions between uropathogens, isolated from elderly individuals suffering from UTIs, and bacteria isolated from the urinary tract of asymptomatic individuals using growth measurements in conditioned media. We observed that bacteria isolated from individuals with UTI-like symptoms and bacteria isolated from asymptomatic individuals can affect each other’s growth; for example, bacteria isolated from symptomatic individuals affect the growth of bacteria isolated from asymptomatic individuals more negatively than vice versa. Additionally, we show that Gram-positive bacteria alter the growth characteristics differently compared to Gram-negative bacteria. Our results are an early step in elucidating the role of microbial interactions in urinary microbial ecosystems that harbor both uropathogens and pre-existing microbiota.

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Section: Methodsmentioning

confidence: 99%

The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens

et al. 2021

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“…Tubes were designed to increase reaction surface to volume ratio [73]. Deformable tubes can achieve both volumes needed for accurate liquid handling as well as the necessary mixing[84] [85]. Peltier devices using highly conductive materials allow with ramp rates of up to 15°C/s heating and 12°C/s cooling [86] [87].…”

Section: B Polymerase Chain Reaction (Pcr)mentioning

confidence: 99%

Navigating the Pandemic Response Life Cycle: Molecular Diagnostics and Immunoassays in the Context of COVID-19 Management

Gharizadeh

Yue

et al. 2021

IEEE Rev. Biomed. Eng.

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Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To counter COVID-19 spreading, an infrastructure to provide rapid and thorough molecular diagnostics and serology testing is the cornerstone of outbreak and pandemic management. We hereby review the clinical insights with regard to using molecular tests and immunoassays in the context of COVID-19 management life cycle: the preventive phase, the preparedness phase, the response phase and the recovery phase. The spatial and temporal distribution of viral RNA, antigens and antibodies during human infection is summarized to provide a biological foundation for accurate detection of the disease. We shared the lessons learned and the obstacles encountered during real world high-volume screening programs. Clinical needs are discussed to identify existing technology gaps in these tests. Leverage technologies, such as engineered polymerases, isothermal amplification, and direct amplification from complex matrices may improve the productivity of current infrastructure, while emerging technologies like CRISPR diagnostics, visual end point detection, and PCR free methods for nucleic acid sensing may lead to at-home tests. The lessons learned, and innovations spurred from the COVID-19 pandemic could upgrade our global public health infrastructure to better combat potential outbreaks in the future.

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“…The phenotypic nature of this technology means it is highly versatile and can be used for a wide range of pathogenic organisms (Gram-positive or -negative bacteria) including ‘slower’ growing organisms such as M. tuberculosis to provide a rapid time-to-result for AST. Furthermore, our method has high-sensitivity enabling detection of E. coli at clinically relevant concentrations, given the UTI bacterial threshold is ≥

CFU/mL, and typically anywhere up to

CFU/mL, and E. coli is the most common uropathogen [ 38 , 39 ]. Further work will look to improve test sensitivity down to at least 10 5 CFU/mL, but the technology is currently well within the acceptable range for a positive UTI diagnosis.…”

Section: Resultsmentioning

confidence: 99%

Development of a Rapid, Antimicrobial Susceptibility Test for E. coli Based on Low-Cost, Screen-Printed Electrodes

et al. 2020

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Antibiotic resistance has been cited by the World Health Organisation (WHO) as one of the greatest threats to public health. Mitigating the spread of antibiotic resistance requires a multipronged approach with possible interventions including faster diagnostic testing and enhanced antibiotic stewardship. This study employs a low-cost diagnostic sensor test to rapidly pinpoint the correct antibiotic for treatment of infection. The sensor comprises a screen-printed gold electrode, modified with an antibiotic-seeded hydrogel to monitor bacterial growth. Electrochemical growth profiles of the common microorganism, Escherichia coli (E. coli) (ATCC 25922) were measured in the presence and absence of the antibiotic streptomycin. Results show a clear distinction between the E. coli growth profiles depending on whether streptomycin is present, in a timeframe of ≈2.5 h (p < 0.05), significantly quicker than the current gold standard of culture-based antimicrobial susceptibility testing. These results demonstrate a clear pathway to a low cost, phenotypic and reproducible antibiotic susceptibility testing technology for the rapid detection of E. coli within clinically relevant concentration ranges for conditions such as urinary tract infections.

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Fast identification of Escherichia coli in urinary tract infections using a virulence gene based PCR approach in a novel thermal cycler

Cited by 30 publications

References 47 publications

The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens

The Good and the Bad: Ecological Interaction Measurements Between the Urinary Microbiota and Uropathogens

Navigating the Pandemic Response Life Cycle: Molecular Diagnostics and Immunoassays in the Context of COVID-19 Management

Development of a Rapid, Antimicrobial Susceptibility Test for E. coli Based on Low-Cost, Screen-Printed Electrodes

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